Whole Genome Sequence Analysis of the Plasma Proteome in Black Adults Provides Novel Insights Into Cardiovascular Disease

Abstract

Background: Plasma proteins are critical mediators of cardiovascular processes and are the targets of many drugs. Previous efforts to characterize the genetic architecture of the plasma proteome have been limited by a focus on individuals of European descent and leveraged genotyping arrays and imputation. Here we describe whole genome sequence analysis of the plasma proteome in individuals with greater African ancestry, increasing our power to identify novel genetic determinants.

Methods: Proteomic profiling of 1301 proteins was performed in 1852 Black adults from the Jackson Heart Study using aptamer-based proteomics (SomaScan). Whole genome sequencing association analysis was ascertained for all variants with minor allele count ≥5. Results were validated using an alternative, antibody-based, proteomic platform (Olink) as well as replicated in the Multi-Ethnic Study of Atherosclerosis and the HERITAGE Family Study (Health, Risk Factors, Exercise Training and Genetics).

Results: We identify 569 genetic associations between 479 proteins and 438 unique genetic regions at a Bonferroni-adjusted significance level of 3.8×10^-11. These associations include 114 novel locus-protein relationships and an additional 217 novel sentinel variant-protein relationships. Novel cardiovascular findings include new protein associations at the APOE gene locus including ZAP70 (sentinel single nucleotide polymorphism [SNP] rs7412-T, β=0.61±0.05, P=3.27×10^-30) and MMP-3 (β=-0.60±0.05, P=1.67×10^-32), as well as a completely novel pleiotropic locus at the HPX gene, associated with 9 proteins. Further, the associations suggest new mechanisms of genetically mediated cardiovascular disease linked to African ancestry; we identify a novel association between variants linked to APOL1-associated chronic kidney and heart disease and the protein CKAP2 (rs73885319-G, β=0.34±0.04, P=1.34×10^-17) as well as an association between ATTR amyloidosis and RBP4 levels in community-dwelling individuals without heart failure.

Conclusions: Taken together, these results provide evidence for the functional importance of variants in non-European populations, and suggest new biological mechanisms for ancestry-specific determinants of lipids, coagulation, and myocardial function.

Keywords: cardiovascular disease; genetics; proteomics; race and ethnicity.

Figure 1.. Chromosomal locations of 569 protein quantitative trait loci.

The locations of the protein quantitative trait loci are indicated on the x-axis while location of the gene encoding that protein is indicated on the y-axis. Locations of genes associated with many proteins are indicated above the plot. Cis associations align along the identity line, while trans associations are off the line.

Figure 2.. Summary of protein quantitative trait loci.

a, Significance level of cis associations according to distance from transcription start site for the cognate gene. b, Number of loci associated with each protein. c, Number of proteins associated with each locus. d,e, Proportion of pQTLs within and between genes, and by GENCODE comprehensive category for each pQTL, darker bars represent novel variant-protein associations. f, Absolute effect size versus minor allele frequency. Small circles indicate known sentinel variant-protein associations, large circles are novel associations. SNPs: single nucleotide polymorphisms. “Exact” indicates that the variant-protein association has been previously identified. “Novel” indicates that the variant-protein associations is novel.

Figure 3.. Ancestry specific reference allele frequencies for each sentinel variant.

Allele frequency in gnomAD among those of African ancestry compared to Non-Finnish European (NFE) ancestry for all 464 unique sentinel variants. As many variants are rare among NFE individuals, a zoomed in subset is provided with African ancestry disease specific variants labeled. TTR = transthyretin.

Figure 4.. In trans associations for novel pleiotropic protein quantitative trait loci.

Two pleiotropic loci with new protein associations: HPX (blue) and APOE (red). The thickness of the lines indicates the relative strength of the association.

Figure 5.. Ancestry specific genetic disease variants and protein levels.

a, TTRm carrier status (rs76992529) and log-scaled RB4 levels. b, APOL1*G1 haplotype status and log-scaled CKAP2 levels